## Loading required package: assertthat
## 
## Attaching package: 'assertthat'
## The following object is masked from 'package:tibble':
## 
##     has_name
## Loading required package: glue
## 
## Attaching package: 'glue'
## The following object is masked from 'package:dplyr':
## 
##     collapse
## Loading required package: rlang
## Warning: package 'rlang' was built under R version 4.0.3
## 
## Attaching package: 'rlang'
## The following object is masked from 'package:assertthat':
## 
##     has_name
## The following objects are masked from 'package:purrr':
## 
##     %@%, as_function, flatten, flatten_chr, flatten_dbl, flatten_int,
##     flatten_lgl, flatten_raw, invoke, list_along, modify, prepend,
##     splice
## 
## -- Column specification --------------------------------------------------------
## cols(
##   id = col_double(),
##   code = col_character(),
##   naam_nederlands = col_character(),
##   naam_wetenschappelijk = col_character(),
##   taxn_vrs_key = col_character(),
##   taxongroep = col_character(),
##   usageKey = col_double(),
##   scientificName = col_character(),
##   rank = col_character(),
##   order = col_character(),
##   matchType = col_character(),
##   phylum = col_character(),
##   kingdom = col_character(),
##   genus = col_character(),
##   class = col_character(),
##   confidence = col_double(),
##   synonym = col_logical(),
##   status = col_character(),
##   family = col_character()
## )
## i Using ',' as decimal and '.' as grouping mark. Use `read_delim()` for more control.
## 
## -- Column specification --------------------------------------------------------
## cols(
##   substraat = col_character(),
##   substrate = col_character()
## )

Exploratory data analysis

## `summarise()` ungrouping output (override with `.groups` argument)
phylum n_obs n_soorten n_hokken
Anthocerotophyta 218 4 123
Bryophyta 95349 410 796
Marchantiophyta 17462 109 727

## `summarise()` regrouping output by 'phylum' (override with `.groups` argument)
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Alternative Telfer method

Goed onderzocht = 40 of meer soorten in een uurhok per periode

Uurhok moet in beide perioden goed onderzocht zijn.

## Joining, by = "substraat"
phylum substrate number of species
Bryophyta artificial stone 84
Bryophyta bryophyte 3
Bryophyta decaying vegetation 21
Bryophyta decorticated wood 48
Bryophyta epiphytic on living wood 73
Bryophyta floating on water 1
Bryophyta gravel or sand 106
Bryophyta mineral soil 210
Bryophyta peat 46
Bryophyta rock, hard 95
Bryophyta rock, soft 38
Bryophyta soil on rock 68
Marchantiophyta artificial stone 9
Marchantiophyta bryophyte 17
Marchantiophyta decaying vegetation 18
Marchantiophyta decorticated wood 16
Marchantiophyta epiphytic on living wood 15
Marchantiophyta floating on water 3
Marchantiophyta gravel or sand 34
Marchantiophyta mineral soil 67
Marchantiophyta peat 30
Marchantiophyta rock, hard 14
Marchantiophyta rock, soft 14
Marchantiophyta soil on rock 20
phylum ell_l number of species
Bryophyta 1 9
Bryophyta 2 19
Bryophyta 3 37
Bryophyta 4 86
Bryophyta 5 125
Bryophyta 6 188
Bryophyta 7 188
Bryophyta 8 126
Bryophyta 9 15
Marchantiophyta 1 1
Marchantiophyta 3 20
Marchantiophyta 4 51
Marchantiophyta 5 51
Marchantiophyta 6 60
Marchantiophyta 7 56
Marchantiophyta 8 18
phylum ell_r number of species
Bryophyta 1 10
Bryophyta 2 63
Bryophyta 3 88
Bryophyta 4 67
Bryophyta 5 95
Bryophyta 6 138
Bryophyta 7 214
Bryophyta 8 101
Bryophyta 9 17
Marchantiophyta 1 28
Marchantiophyta 2 60
Marchantiophyta 3 20
Marchantiophyta 4 52
Marchantiophyta 5 30
Marchantiophyta 6 38
Marchantiophyta 7 21
Marchantiophyta 8 6
Marchantiophyta 9 2
phylum ell_f number of species
Bryophyta 1 12
Bryophyta 2 12
Bryophyta 3 61
Bryophyta 4 152
Bryophyta 5 187
Bryophyta 6 176
Bryophyta 7 50
Bryophyta 8 69
Bryophyta 9 51
Bryophyta 10 14
Bryophyta 11 4
Bryophyta 12 5
Marchantiophyta 4 15
Marchantiophyta 5 51
Marchantiophyta 6 52
Marchantiophyta 7 50
Marchantiophyta 8 47
Marchantiophyta 9 32
Marchantiophyta 10 9
Marchantiophyta 11 1
phylum ell_n number of species
Bryophyta 1 32
Bryophyta 2 192
Bryophyta 3 139
Bryophyta 4 195
Bryophyta 5 137
Bryophyta 6 71
Bryophyta 7 27
Marchantiophyta 1 43
Marchantiophyta 2 97
Marchantiophyta 3 45
Marchantiophyta 4 36
Marchantiophyta 5 23
Marchantiophyta 6 8
Marchantiophyta 7 5
phylum ell_t number of species
Bryophyta 2 48
Bryophyta 3 269
Bryophyta 4 142
Bryophyta 5 155
Bryophyta 6 108
Bryophyta 7 58
Bryophyta 8 13
Marchantiophyta 2 27
Marchantiophyta 3 113
Marchantiophyta 4 51
Marchantiophyta 5 43
Marchantiophyta 6 13
Marchantiophyta 7 2
Marchantiophyta 8 8

Only remove substrate levels with less than 5 species (for Ellenberg variables this is not necessary because they are included as continuous covariate).

## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2

phylum substrate n
Bryophyta artificial stone 84
Bryophyta decaying vegetation 21
Bryophyta decorticated wood 48
Bryophyta epiphytic on living wood 73
Bryophyta gravel or sand 106
Bryophyta mineral soil 210
Bryophyta peat 46
Bryophyta rock, hard 95
Bryophyta rock, soft 38
Bryophyta soil on rock 68
Marchantiophyta artificial stone 9
Marchantiophyta bryophyte 17
Marchantiophyta decaying vegetation 18
Marchantiophyta decorticated wood 16
Marchantiophyta epiphytic on living wood 15
Marchantiophyta gravel or sand 34
Marchantiophyta mineral soil 67
Marchantiophyta peat 30
Marchantiophyta rock, hard 14
Marchantiophyta rock, soft 14
Marchantiophyta soil on rock 20
## Warning: Ignoring unknown aesthetics: text
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: `group_by_()` is deprecated as of dplyr 0.7.0.
## Please use `group_by()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## # A tibble: 124 x 2
##    `n_hok_1980-1999`     n
##                <int> <int>
##  1                 0   241
##  2                 5    35
##  3                 6    17
##  4                 7    18
##  5                 8    12
##  6                 9    22
##  7                10    14
##  8                11    12
##  9                12    15
## 10                13     4
## # ... with 114 more rows
## # A tibble: 145 x 2
##    `n_hok_2000-2019`     n
##                <int> <int>
##  1                 0    18
##  2                 1    86
##  3                 2    63
##  4                 3    33
##  5                 4    39
##  6                 5    20
##  7                 6    22
##  8                 7    14
##  9                 8    25
## 10                 9    16
## # ... with 135 more rows

Keeping only species that occur in both periods (much improves model validation). (Alternative could be to include a factor with levels for lost, persisting, gained in the model to explain lost and gained species, but maybe see this as a separate model with the full dataset!)

Overdispersion (residual deviance divided by residual degrees of freedom >> 1)! Quasi-binomial model needed.

Should we include interaction between baseline proportion and substrate or ellenberg variables?

## 
## Call:
## glm(formula = cbind(`n_hok_2000-2019` + 1, `n_hok_tot_2000-2019` - 
##     `n_hok_2000-2019` - 1) ~ qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`) + 
##     phylum + qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum + 
##     (substrate + ell_l + ell_n + ell_f + ell_t) * phylum, family = "quasibinomial", 
##     data = analyse_data_telfer_agg)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -13.3930   -2.4523   -0.5277    1.7451   11.5813  
## 
## Coefficients: (1 not defined because of singularities)
##                                                                              Estimate
## (Intercept)                                                                  0.581124
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)                        0.932018
## phylumMarchantiophyta                                                       -0.436164
## substratebryophyte                                                          -0.234983
## substratedecaying vegetation                                                 0.069042
## substratedecorticated wood                                                   0.079133
## substrateepiphytic on living wood                                            0.440749
## substrategravel or sand                                                     -0.006071
## substratemineral soil                                                       -0.063548
## substratepeat                                                                0.193737
## substraterock, hard                                                          0.129607
## substraterock, soft                                                          0.026071
## substratesoil on rock                                                        0.043359
## ell_l                                                                       -0.019053
## ell_n                                                                       -0.029888
## ell_f                                                                       -0.063934
## ell_t                                                                        0.041822
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta  0.021463
## phylumMarchantiophyta:substratebryophyte                                           NA
## phylumMarchantiophyta:substratedecaying vegetation                          -0.237880
## phylumMarchantiophyta:substratedecorticated wood                            -0.369963
## phylumMarchantiophyta:substrateepiphytic on living wood                      0.233065
## phylumMarchantiophyta:substrategravel or sand                               -0.217055
## phylumMarchantiophyta:substratemineral soil                                 -0.198928
## phylumMarchantiophyta:substratepeat                                         -0.294218
## phylumMarchantiophyta:substraterock, hard                                   -0.412046
## phylumMarchantiophyta:substraterock, soft                                   -0.061837
## phylumMarchantiophyta:substratesoil on rock                                  0.053290
## phylumMarchantiophyta:ell_l                                                 -0.018365
## phylumMarchantiophyta:ell_n                                                  0.021410
## phylumMarchantiophyta:ell_f                                                 -0.024859
## phylumMarchantiophyta:ell_t                                                  0.101384
##                                                                             Std. Error
## (Intercept)                                                                   0.207479
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)                         0.020002
## phylumMarchantiophyta                                                         0.498275
## substratebryophyte                                                            0.355548
## substratedecaying vegetation                                                  0.178141
## substratedecorticated wood                                                    0.131272
## substrateepiphytic on living wood                                             0.119177
## substrategravel or sand                                                       0.115150
## substratemineral soil                                                         0.101872
## substratepeat                                                                 0.145852
## substraterock, hard                                                           0.123034
## substraterock, soft                                                           0.160941
## substratesoil on rock                                                         0.125512
## ell_l                                                                         0.019759
## ell_n                                                                         0.022669
## ell_f                                                                         0.017658
## ell_t                                                                         0.023228
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.050436
## phylumMarchantiophyta:substratebryophyte                                            NA
## phylumMarchantiophyta:substratedecaying vegetation                            0.366808
## phylumMarchantiophyta:substratedecorticated wood                              0.364577
## phylumMarchantiophyta:substrateepiphytic on living wood                       0.385011
## phylumMarchantiophyta:substrategravel or sand                                 0.322868
## phylumMarchantiophyta:substratemineral soil                                   0.300539
## phylumMarchantiophyta:substratepeat                                           0.340603
## phylumMarchantiophyta:substraterock, hard                                     0.395109
## phylumMarchantiophyta:substraterock, soft                                     0.383068
## phylumMarchantiophyta:substratesoil on rock                                   0.335821
## phylumMarchantiophyta:ell_l                                                   0.041151
## phylumMarchantiophyta:ell_n                                                   0.052353
## phylumMarchantiophyta:ell_f                                                   0.045773
## phylumMarchantiophyta:ell_t                                                   0.053381
##                                                                             t value
## (Intercept)                                                                   2.801
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)                        46.596
## phylumMarchantiophyta                                                        -0.875
## substratebryophyte                                                           -0.661
## substratedecaying vegetation                                                  0.388
## substratedecorticated wood                                                    0.603
## substrateepiphytic on living wood                                             3.698
## substrategravel or sand                                                      -0.053
## substratemineral soil                                                        -0.624
## substratepeat                                                                 1.328
## substraterock, hard                                                           1.053
## substraterock, soft                                                           0.162
## substratesoil on rock                                                         0.345
## ell_l                                                                        -0.964
## ell_n                                                                        -1.318
## ell_f                                                                        -3.621
## ell_t                                                                         1.800
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.426
## phylumMarchantiophyta:substratebryophyte                                         NA
## phylumMarchantiophyta:substratedecaying vegetation                           -0.649
## phylumMarchantiophyta:substratedecorticated wood                             -1.015
## phylumMarchantiophyta:substrateepiphytic on living wood                       0.605
## phylumMarchantiophyta:substrategravel or sand                                -0.672
## phylumMarchantiophyta:substratemineral soil                                  -0.662
## phylumMarchantiophyta:substratepeat                                          -0.864
## phylumMarchantiophyta:substraterock, hard                                    -1.043
## phylumMarchantiophyta:substraterock, soft                                    -0.161
## phylumMarchantiophyta:substratesoil on rock                                   0.159
## phylumMarchantiophyta:ell_l                                                  -0.446
## phylumMarchantiophyta:ell_n                                                   0.409
## phylumMarchantiophyta:ell_f                                                  -0.543
## phylumMarchantiophyta:ell_t                                                   1.899
##                                                                             Pr(>|t|)
## (Intercept)                                                                 0.005227
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)                        < 2e-16
## phylumMarchantiophyta                                                       0.381663
## substratebryophyte                                                          0.508877
## substratedecaying vegetation                                                0.698444
## substratedecorticated wood                                                  0.546810
## substrateepiphytic on living wood                                           0.000233
## substrategravel or sand                                                     0.957966
## substratemineral soil                                                       0.532947
## substratepeat                                                               0.184478
## substraterock, hard                                                         0.292487
## substraterock, soft                                                         0.871357
## substratesoil on rock                                                       0.729846
## ell_l                                                                       0.335211
## ell_n                                                                       0.187753
## ell_f                                                                       0.000314
## ell_t                                                                       0.072183
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.670552
## phylumMarchantiophyta:substratebryophyte                                          NA
## phylumMarchantiophyta:substratedecaying vegetation                          0.516850
## phylumMarchantiophyta:substratedecorticated wood                            0.310540
## phylumMarchantiophyta:substrateepiphytic on living wood                     0.545130
## phylumMarchantiophyta:substrategravel or sand                               0.501618
## phylumMarchantiophyta:substratemineral soil                                 0.508234
## phylumMarchantiophyta:substratepeat                                         0.387965
## phylumMarchantiophyta:substraterock, hard                                   0.297345
## phylumMarchantiophyta:substraterock, soft                                   0.871801
## phylumMarchantiophyta:substratesoil on rock                                 0.873960
## phylumMarchantiophyta:ell_l                                                 0.655514
## phylumMarchantiophyta:ell_n                                                 0.682692
## phylumMarchantiophyta:ell_f                                                 0.587223
## phylumMarchantiophyta:ell_t                                                 0.057912
##                                                                                
## (Intercept)                                                                 ** 
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)                       ***
## phylumMarchantiophyta                                                          
## substratebryophyte                                                             
## substratedecaying vegetation                                                   
## substratedecorticated wood                                                     
## substrateepiphytic on living wood                                           ***
## substrategravel or sand                                                        
## substratemineral soil                                                          
## substratepeat                                                                  
## substraterock, hard                                                            
## substraterock, soft                                                            
## substratesoil on rock                                                          
## ell_l                                                                          
## ell_n                                                                          
## ell_f                                                                       ***
## ell_t                                                                       .  
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylumMarchantiophyta    
## phylumMarchantiophyta:substratebryophyte                                       
## phylumMarchantiophyta:substratedecaying vegetation                             
## phylumMarchantiophyta:substratedecorticated wood                               
## phylumMarchantiophyta:substrateepiphytic on living wood                        
## phylumMarchantiophyta:substrategravel or sand                                  
## phylumMarchantiophyta:substratemineral soil                                    
## phylumMarchantiophyta:substratepeat                                            
## phylumMarchantiophyta:substraterock, hard                                      
## phylumMarchantiophyta:substraterock, soft                                      
## phylumMarchantiophyta:substratesoil on rock                                    
## phylumMarchantiophyta:ell_l                                                    
## phylumMarchantiophyta:ell_n                                                    
## phylumMarchantiophyta:ell_f                                                    
## phylumMarchantiophyta:ell_t                                                 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasibinomial family taken to be 13.31708)
## 
##     Null deviance: 86097.7  on 783  degrees of freedom
## Residual deviance:  9531.1  on 753  degrees of freedom
## AIC: NA
## 
## Number of Fisher Scoring iterations: 4
## Analysis of Deviance Table
## 
## Model: quasibinomial, link: logit
## 
## Response: cbind(`n_hok_2000-2019` + 1, `n_hok_tot_2000-2019` - `n_hok_2000-2019` - 1)
## 
## Terms added sequentially (first to last)
## 
## 
##                                                              Df Deviance
## NULL                                                                    
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)         1    74063
## phylum                                                        1     1075
## substrate                                                    10      755
## ell_l                                                         1        6
## ell_n                                                         1        8
## ell_f                                                         1      312
## ell_t                                                         1      111
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum  1       10
## phylum:substrate                                              9      128
## phylum:ell_l                                                  1        3
## phylum:ell_n                                                  1       33
## phylum:ell_f                                                  1       14
## phylum:ell_t                                                  1       48
##                                                              Resid. Df
## NULL                                                               783
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)              782
## phylum                                                             781
## substrate                                                          771
## ell_l                                                              770
## ell_n                                                              769
## ell_f                                                              768
## ell_t                                                              767
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum       766
## phylum:substrate                                                   757
## phylum:ell_l                                                       756
## phylum:ell_n                                                       755
## phylum:ell_f                                                       754
## phylum:ell_t                                                       753
##                                                              Resid. Dev
## NULL                                                              86098
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)             12035
## phylum                                                            10959
## substrate                                                         10205
## ell_l                                                             10198
## ell_n                                                             10191
## ell_f                                                              9878
## ell_t                                                              9767
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum       9757
## phylum:substrate                                                   9630
## phylum:ell_l                                                       9626
## phylum:ell_n                                                       9593
## phylum:ell_f                                                       9579
## phylum:ell_t                                                       9531
##                                                                      F
## NULL                                                                  
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)        5561.5162
## phylum                                                         80.7531
## substrate                                                       5.6670
## ell_l                                                           0.4553
## ell_n                                                           0.5785
## ell_f                                                          23.4477
## ell_t                                                           8.3418
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum    0.7478
## phylum:substrate                                                1.0669
## phylum:ell_l                                                    0.2609
## phylum:ell_n                                                    2.4779
## phylum:ell_f                                                    1.0325
## phylum:ell_t                                                    3.6259
##                                                                 Pr(>F)    
## NULL                                                                      
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`)        < 2.2e-16 ***
## phylum                                                       < 2.2e-16 ***
## substrate                                                    3.258e-08 ***
## ell_l                                                         0.500035    
## ell_n                                                         0.447137    
## ell_f                                                        1.558e-06 ***
## ell_t                                                         0.003985 ** 
## qlogis((`n_hok_1980-1999` + 1)/`n_hok_tot_1980-1999`):phylum  0.387447    
## phylum:substrate                                              0.385079    
## phylum:ell_l                                                  0.609654    
## phylum:ell_n                                                  0.115877    
## phylum:ell_f                                                  0.309902    
## phylum:ell_t                                                  0.057269 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Call:
## glm(formula = cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` - 
##     `n_hok_2000-2019`) ~ qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) + 
##     phylum + qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum + 
##     substrate + phylum:substrate, family = "quasibinomial", data = analyse_data_telfer_agg)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -13.4252   -2.4596   -0.4555    1.8609   13.7597  
## 
## Coefficients: (1 not defined because of singularities)
##                                                                         Estimate
## (Intercept)                                                              0.19747
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        0.93289
## phylumMarchantiophyta                                                   -0.19266
## substratebryophyte                                                      -0.44616
## substratedecaying vegetation                                             0.02417
## substratedecorticated wood                                               0.05016
## substrateepiphytic on living wood                                        0.47077
## substrategravel or sand                                                 -0.03462
## substratemineral soil                                                   -0.11935
## substratepeat                                                            0.08668
## substraterock, hard                                                      0.12204
## substraterock, soft                                                      0.10029
## substratesoil on rock                                                    0.09399
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta  0.04230
## phylumMarchantiophyta:substratebryophyte                                      NA
## phylumMarchantiophyta:substratedecaying vegetation                      -0.32723
## phylumMarchantiophyta:substratedecorticated wood                        -0.41701
## phylumMarchantiophyta:substrateepiphytic on living wood                  0.18268
## phylumMarchantiophyta:substrategravel or sand                           -0.35145
## phylumMarchantiophyta:substratemineral soil                             -0.21636
## phylumMarchantiophyta:substratepeat                                     -0.33846
## phylumMarchantiophyta:substraterock, hard                               -0.34373
## phylumMarchantiophyta:substraterock, soft                               -0.22809
## phylumMarchantiophyta:substratesoil on rock                             -0.04555
##                                                                         Std. Error
## (Intercept)                                                                0.09194
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                          0.01993
## phylumMarchantiophyta                                                      0.28953
## substratebryophyte                                                         0.35083
## substratedecaying vegetation                                               0.18147
## substratedecorticated wood                                                 0.13395
## substrateepiphytic on living wood                                          0.12532
## substrategravel or sand                                                    0.11758
## substratemineral soil                                                      0.10484
## substratepeat                                                              0.13659
## substraterock, hard                                                        0.12973
## substraterock, soft                                                        0.17017
## substratesoil on rock                                                      0.13238
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta    0.04841
## phylumMarchantiophyta:substratebryophyte                                        NA
## phylumMarchantiophyta:substratedecaying vegetation                         0.37080
## phylumMarchantiophyta:substratedecorticated wood                           0.37424
## phylumMarchantiophyta:substrateepiphytic on living wood                    0.37980
## phylumMarchantiophyta:substrategravel or sand                              0.32816
## phylumMarchantiophyta:substratemineral soil                                0.31053
## phylumMarchantiophyta:substratepeat                                        0.33750
## phylumMarchantiophyta:substraterock, hard                                  0.42152
## phylumMarchantiophyta:substraterock, soft                                  0.40514
## phylumMarchantiophyta:substratesoil on rock                                0.35294
##                                                                         t value
## (Intercept)                                                               2.148
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        46.818
## phylumMarchantiophyta                                                    -0.665
## substratebryophyte                                                       -1.272
## substratedecaying vegetation                                              0.133
## substratedecorticated wood                                                0.374
## substrateepiphytic on living wood                                         3.757
## substrategravel or sand                                                  -0.294
## substratemineral soil                                                    -1.138
## substratepeat                                                             0.635
## substraterock, hard                                                       0.941
## substraterock, soft                                                       0.589
## substratesoil on rock                                                     0.710
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.874
## phylumMarchantiophyta:substratebryophyte                                     NA
## phylumMarchantiophyta:substratedecaying vegetation                       -0.883
## phylumMarchantiophyta:substratedecorticated wood                         -1.114
## phylumMarchantiophyta:substrateepiphytic on living wood                   0.481
## phylumMarchantiophyta:substrategravel or sand                            -1.071
## phylumMarchantiophyta:substratemineral soil                              -0.697
## phylumMarchantiophyta:substratepeat                                      -1.003
## phylumMarchantiophyta:substraterock, hard                                -0.815
## phylumMarchantiophyta:substraterock, soft                                -0.563
## phylumMarchantiophyta:substratesoil on rock                              -0.129
##                                                                         Pr(>|t|)
## (Intercept)                                                             0.032033
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        < 2e-16
## phylumMarchantiophyta                                                   0.505987
## substratebryophyte                                                      0.203850
## substratedecaying vegetation                                            0.894061
## substratedecorticated wood                                              0.708168
## substrateepiphytic on living wood                                       0.000185
## substrategravel or sand                                                 0.768513
## substratemineral soil                                                   0.255308
## substratepeat                                                           0.525886
## substraterock, hard                                                     0.347167
## substraterock, soft                                                     0.555790
## substratesoil on rock                                                   0.477928
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta 0.382446
## phylumMarchantiophyta:substratebryophyte                                      NA
## phylumMarchantiophyta:substratedecaying vegetation                      0.377784
## phylumMarchantiophyta:substratedecorticated wood                        0.265508
## phylumMarchantiophyta:substrateepiphytic on living wood                 0.630664
## phylumMarchantiophyta:substrategravel or sand                           0.284517
## phylumMarchantiophyta:substratemineral soil                             0.486174
## phylumMarchantiophyta:substratepeat                                     0.316251
## phylumMarchantiophyta:substraterock, hard                               0.415071
## phylumMarchantiophyta:substraterock, soft                               0.573601
## phylumMarchantiophyta:substratesoil on rock                             0.897348
##                                                                            
## (Intercept)                                                             *  
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                       ***
## phylumMarchantiophyta                                                      
## substratebryophyte                                                         
## substratedecaying vegetation                                               
## substratedecorticated wood                                                 
## substrateepiphytic on living wood                                       ***
## substrategravel or sand                                                    
## substratemineral soil                                                      
## substratepeat                                                              
## substraterock, hard                                                        
## substraterock, soft                                                        
## substratesoil on rock                                                      
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta    
## phylumMarchantiophyta:substratebryophyte                                   
## phylumMarchantiophyta:substratedecaying vegetation                         
## phylumMarchantiophyta:substratedecorticated wood                           
## phylumMarchantiophyta:substrateepiphytic on living wood                    
## phylumMarchantiophyta:substrategravel or sand                              
## phylumMarchantiophyta:substratemineral soil                                
## phylumMarchantiophyta:substratepeat                                        
## phylumMarchantiophyta:substraterock, hard                                  
## phylumMarchantiophyta:substraterock, soft                                  
## phylumMarchantiophyta:substratesoil on rock                                
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasibinomial family taken to be 14.77914)
## 
##     Null deviance: 86541  on 783  degrees of freedom
## Residual deviance: 10259  on 761  degrees of freedom
## AIC: NA
## 
## Number of Fisher Scoring iterations: 4
## Analysis of Deviance Table
## 
## Model: quasibinomial, link: logit
## 
## Response: cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` - `n_hok_2000-2019`)
## 
## Terms added sequentially (first to last)
## 
## 
##                                                          Df Deviance Resid. Df
## NULL                                                                       783
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)         1    74320       782
## phylum                                                    1     1092       781
## substrate                                                10      764       771
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum  1       15       770
## phylum:substrate                                          9       90       761
##                                                          Resid. Dev         F
## NULL                                                          86541          
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)             12221 5028.7428
## phylum                                                        11128   73.9045
## substrate                                                     10364    5.1726
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum      10349    0.9934
## phylum:substrate                                              10259    0.6787
##                                                             Pr(>F)    
## NULL                                                                  
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)        < 2.2e-16 ***
## phylum                                                   < 2.2e-16 ***
## substrate                                                2.346e-07 ***
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum    0.3192    
## phylum:substrate                                            0.7287    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Call:
## glm(formula = cbind(`n_hok_2000-2019`, `n_hok_tot_2000-2019` - 
##     `n_hok_2000-2019`) ~ qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`) + 
##     phylum + qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylum + 
##     (ell_l + ell_n + ell_f + ell_t) * phylum, family = "quasibinomial", 
##     data = analyse_data_telfer_agg)
## 
## Deviance Residuals: 
##    Min      1Q  Median      3Q     Max  
## -9.824  -2.563  -0.525   1.712  14.203  
## 
## Coefficients:
##                                                                          Estimate
## (Intercept)                                                              0.829980
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        0.922411
## phylumMarchantiophyta                                                   -0.364332
## ell_l                                                                   -0.036997
## ell_n                                                                   -0.027142
## ell_f                                                                   -0.077162
## ell_t                                                                    0.036164
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta  0.043151
## phylumMarchantiophyta:ell_l                                             -0.001829
## phylumMarchantiophyta:ell_n                                              0.066577
## phylumMarchantiophyta:ell_f                                             -0.070417
## phylumMarchantiophyta:ell_t                                              0.062708
##                                                                         Std. Error
## (Intercept)                                                               0.184957
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                         0.019297
## phylumMarchantiophyta                                                     0.374915
## ell_l                                                                     0.018191
## ell_n                                                                     0.021461
## ell_f                                                                     0.016998
## ell_t                                                                     0.023175
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.050779
## phylumMarchantiophyta:ell_l                                               0.038826
## phylumMarchantiophyta:ell_n                                               0.047973
## phylumMarchantiophyta:ell_f                                               0.041641
## phylumMarchantiophyta:ell_t                                               0.052088
##                                                                         t value
## (Intercept)                                                               4.487
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        47.800
## phylumMarchantiophyta                                                    -0.972
## ell_l                                                                    -2.034
## ell_n                                                                    -1.265
## ell_f                                                                    -4.540
## ell_t                                                                     1.560
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.850
## phylumMarchantiophyta:ell_l                                              -0.047
## phylumMarchantiophyta:ell_n                                               1.388
## phylumMarchantiophyta:ell_f                                              -1.691
## phylumMarchantiophyta:ell_t                                               1.204
##                                                                         Pr(>|t|)
## (Intercept)                                                             8.31e-06
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                        < 2e-16
## phylumMarchantiophyta                                                     0.3315
## ell_l                                                                     0.0423
## ell_n                                                                     0.2064
## ell_f                                                                   6.54e-06
## ell_t                                                                     0.1191
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta   0.3957
## phylumMarchantiophyta:ell_l                                               0.9624
## phylumMarchantiophyta:ell_n                                               0.1656
## phylumMarchantiophyta:ell_f                                               0.0912
## phylumMarchantiophyta:ell_t                                               0.2290
##                                                                            
## (Intercept)                                                             ***
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`)                       ***
## phylumMarchantiophyta                                                      
## ell_l                                                                   *  
## ell_n                                                                      
## ell_f                                                                   ***
## ell_t                                                                      
## qlogis((`n_hok_1980-1999`)/`n_hok_tot_1980-1999`):phylumMarchantiophyta    
## phylumMarchantiophyta:ell_l                                                
## phylumMarchantiophyta:ell_n                                                
## phylumMarchantiophyta:ell_f                                             .  
## phylumMarchantiophyta:ell_t                                                
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasibinomial family taken to be 13.90762)
## 
##     Null deviance: 86541  on 783  degrees of freedom
## Residual deviance: 10273  on 772  degrees of freedom
## AIC: NA
## 
## Number of Fisher Scoring iterations: 4

Models including substrate are rank-deficient and the fit may be misleading…

## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading

Same figure but this time in link-scale (to obtain Telfer-like figures):

## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading

## Warning in predict.lm(object, newdata, se.fit, scale = residual.scale, type = if
## (type == : prediction from a rank-deficient fit may be misleading